You have 2 routes you can take, not knowing the stage your car is at, and how much time/effort you want to apply? but if the vehicle is in the "restoration/refurbishing" phase, Option 1, I would reset/shim the plug to bring it almost flush with the roof skin IF it's lower than 1/8" in the larger window channel, and finish it in with the fillers I listed above, if done properly you should have a slim taper of filler from the SE window trim perimeter to an 1/8" max thickness to the plug/roof transition area/perimeter, then you can glue the vinyl to the plug and basically treat the roof and plug as the same...

option 2 is to do as the factory did and tape/foam mask the plug to create a "padded" area around the rear window, then you DON't glue the vinyl to the foam padding just the metal surrounding roof areas around the plug and the bare widow channel of the plug, the vinyl over the foam will basically "hover"....eventually UV/sun heat/age the vinyl around the plug will shrink/stretch at a greater rate than that glued to the steel roof and you'll see telegraphing of the plug/foam/tape

Personally I'd opt for option 1 for long term stability of the vinyl roof, unless OEM is your goal, as far as the cellular foam, any good fabric/marine-automotive/upholstery shop should have various thickness to choose from

Mike